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  • 1.
    Aurell, Erik
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Aalto University, Finland.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). The Hebrew University of Jerusalem, Israel.
    Zhou, Hai-Jun
    State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China.
    The bulk and the tail of minimal absent words in genome sequences2016Inngår i: Physical Biology, ISSN 1478-3967, E-ISSN 1478-3975, Vol. 13, nr 2, artikkel-id 026004Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whether the reason behind this phenomenon is statistical or reflects a biological mechanism, and what biological information is contained in absent words. % In this work we demonstrate that the bulk can be described by a probabilistic model of sampling words from random sequences, while the tail of long MAWs is of biological origin. We introduce the novel concept of a core of a minimal absent word, which are sequences present in the genome and closest to a given MAW. We show that in bacteria and yeast the cores of the longest MAWs, which exist in two or more copies, are located in highly conserved regions the most prominent example being ribosomal RNAs (rRNAs). We also show that while the distribution of the cores of long MAWs is roughly uniform over these genomes on a coarse-grained level, on a more detailed level it is strongly enhanced in 3' untranslated regions (UTRs) and, to a lesser extent, also in 5' UTRs. This indicates that MAWs and associated MAW cores correspond to fine-tuned evolutionary relationships, and suggest that they can be more widely used as markers for genomic complexity.

  • 2.
    Bogdanowicz, Janusz
    et al.
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Gilbert, Matthieu
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Skolan för elektro- och systemteknik (EES), Centra, Alfvénlaboratoriet.
    Koelling, Sebastian
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Vanderheyden, Benoit
    4 Institut Montefiore, Sart-Tilman B28, B-4000 Liege, Belgium.
    Vandervorst, Wilfried
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Light absorption in conical silicon particles2013Inngår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 21, nr 3, s. 3891-3896Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The problem of the absorption of light by a nanoscale dielectric cone is discussed. A simplified solution based on the analytical Mie theory of scattering and absorption by cylindrical objects is proposed and supported by the experimental observation of sharply localized holes in conical silicon tips after high-fluence irradiation. This study reveals that light couples with tapered objects dominantly at specific locations, where the local radius corresponds to one of the resonant radii of a cylindrical object, as predicted by Mie theory.

  • 3.
    Chatterjee, Saikat
    et al.
    KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    Koslicki, David
    Dept of Mathematics, Oregon State University, Corvallis, USA.
    Dong, Siyuan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Cheng, Lu
    Dept of Mathematics and Statistics, University of Helsinki, Finland.
    Lan, Yueheng
    Dept of Physics, Tsinghua University, Beijing, China.
    Vehkaperä, Mikko
    KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    Skoglund, Mikael
    KTH, Skolan för elektro- och systemteknik (EES), Centra, ACCESS Linnaeus Centre. KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    K. Rasmussen, Lars
    KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Corander, Jukka
    Dept of Signal Processing, Aalto University, Finland.
    SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition2014Inngår i: Bioinformatics, ISSN 1460-2059, Vol. 30, nr 17, s. 2423-2431Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically time-consuming in a desktop computing environment.

    Results: Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task, and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method, which is shown to be more robust to input data variation than a recently introduced related method.

    Availability and implementation: A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above Web site.

  • 4.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Data Analysis and Next Generation Sequencing : Applications in Microbiology.2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Next Generation Sequencing (NGS) is a new technology that has revolutionized the way we study living organisms. Where previously only a few genes could be studied at a time through targeted direct probing, NGS offers the possibility to perform measurements for a whole genome at once. The drawback is that the amount of data generated in the process is large and extracting useful information from it requires new methods to process and analyze it.

    The main contribution of this thesis is the development of a novel experimental method coined tagRNA-seq, combining 5’tagRACE, a previously developed technique, with RNA-sequencing technology. Briefly, tagRNA-seq makes it possible to identify the 5’ ends of RNAs in bacteria and directly probe for their type, primary or processed, by ligating short RNA sequences, the tags, to the beginnings of RNA molecules. We used the method to directly probe for transcription start and processing sites in two bacterial species, Escherichiacoli and Enterococcus faecalis. It was also used to study polyadenylation in E. coli, where the ability to identify processed RNA molecules proved to be useful to separate direct and indirect regulatory effects of this mechanism. We also demonstrate how data from tagRNA-seq experiments can be used to increase confidence on the discovery of anti-sense transcripts in bacteria. Analyses of RNA-seq data obtained in the context of these experiments revealed subtle artifacts in the coverage signal towards gene ends, that we were able to explain and quantify based Kolmogorov’s broken stick model. We also discovered evidences for circularization of a few RNA transcripts, both in our own data sets and publicly available data.

    Designing the tags used in tagRNA-seq led us to the problem of words absent from a text. We focus on a particular subset of these, the minimal absent words (MAWs), and develop a theory providing a complete description of their size distribution in random text. We also show that MAWs in genomes from viruses and living organisms almost always exhibit a behavior different from random texts in the tail of the distribution, and that MAWs from this tail are closely related to sequences present in the genome that preferentially appear in regions with important regulatory functions.

    Finally, and independently from tagRNA-seq, we propose a new approach to the problem of bacterial community reconstruction in metagenomic, based on techniques from compressed sensing. We provide a novel algorithm competing with state-of-the-art techniques in the field.

  • 5.
    Innocenti, Nicolas
    University of Liège.
    Interaction of femtosecond laser pulses with nanoscaleSi-tips for atom probe tomography2010Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The atom probe is an analysis technique based on the emission of ionized species from a needle-shaped sample (apex radius < 100 nm) under the influence of a very strong electric field ( 10-50 V/nm). A DC-voltage is applied on the sample in order to generate a field slightly below the one necessary to remove atoms (in the form of ions) from its surface. An ultrashort (femtosecond) laser pulse is used to trigger the emission. The evaporated ions are accelerated in the electric field and projected onto a position sensitive detector where a magnified image of the surface is formed (magnication from 10^6 to 10^7). Time of flight mass spectrometry is used to chemically identify the evaporated atoms. The technique thus allows to analyze the composition of a 3D volume with sub-nanometer resolution. Imec conducts research in order to introduce the 3D characterization with quasi-atomic resolution capabilities of the technique to the semiconductor industry. It became quickly apparent that a detailed understanding of the laser interaction with the nanoscale samples is crucial in order to interpret the analysis results. In this work, we briefly introduce the principles of the technique and review some of its applications. We then summarize some of the currently unexplained experimental observations, taken from the literature or from experiments conducted at Imec. Based on those observations, we introduce a thermally assisted model of field evaporation that includes the electromagnetic nature of light and the semiconducting character of silicon. The optical absorption of the nanoscale sample is computed by numerical simulations using the FDTD algorithm. The temperature evolution at the tip apex is obtained by solving a coupled thermal conduction-carrier recombinations problem and the shape of the mass spectrum is deduced. We discuss the model and confront its results to experimental data. We show that the model qualitatively explains many experimental aspects of the characterization of silicon by means of an atom probe analysis. Nevertheless, we show that at this stage the model lacks quantitative accuracy and we suggest several ways to improve it.

  • 6.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Skolan för informations- och kommunikationsteknik (ICT), Mikroelektronik och tillämpad fysik, MAP.
    What microcavities can do in photonics : coupling resonances and optical gain2009Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The present master's thesis deals with numerical modeling of solid-state micrometrical-sized polymeric dye lasers, commonly denoted as microcavities. It is part of a large research initiative carried out in the optics group, at the MAP (Microelectronics and Applied Physics) department in KTH (Kungliga Tekniska Högskolan - Royal Technical School) and targeted towards the design and manufacturing of micro- and nano-scaled polymeric components for nano-photonics, primarily lasers. The finite element method (FEM) in frequency domain is used as a primary modeling tool through the simulation software COMSOL Multiphysics. Models for spontaneous emission, optical losses and gain are developed and demonstrated. A specic layout is studied: the double hexagonal microcavity. While it was expected to be a good candidate for a laser, the design shows unexpected properties making it useful for sensing applications. Finally, the transposition of models to time domain is initiated : a replacement solution for the lacking perfectly matched layer (PML) in Comsol is developed and demonstrated. Methods for modeling materials parameters in time domain are investigated, together with the possible use of a more suitable algorithm : finite dierences in time domain (FDTD) or Yee's scheme.

  • 7.
    Innocenti, Nicolas
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends2013Inngår i: Journal of Statistical Mechanics: Theory and Experiment, ISSN 1742-5468, E-ISSN 1742-5468, Vol. 2013, nr 10, s. P10013-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    High-throughput transcriptomics experiments have reached the stage where the count of the number of reads alignable to a given position can be treated as an almost-continuous signal. This allows us to ask questions of biophysical/biotechnical nature, but which may still have biological implications. Here we show that when sequencing RNA fragments from one end, as is the case on most platforms, an oscillation in the read count is observed at the other end. We further show that these oscillations can be well described by Kolmogorov's 1941 broken stick model. We investigate how the model can be used to improve predictions of gene ends (3' transcript ends), but conclude that with present data the improvement is only marginal. The results highlight subtle effects in high-throughput transcriptomics experiments which do not have a biological origin, but which may still be used to obtain biological information.

  • 8.
    Innocenti, Nicolas
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Golumbeanu, Monica
    Department of Biosystems Science and Engineering, ETH Zürich, CH-4058, Basel, Switzerland.
    Fouquier d'Hérouël, Aymeric
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg.
    Lacoux, Caroline
    INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.
    Bonnin, Rémy A.
    Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France.
    Kennedy, Sean P.
    INRA, MetaGenoPolis US1367, Domaine de Vilvert, F-78350, Jouy-en-Josas, France.
    Wessner, Francoise
    INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.
    Serror, Pascale
    INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.
    Bouloc, Philippe
    Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France.
    Repoila, Francis
    INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis2015Inngår i: RNA, ISSN 1355-8382Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5' RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA-and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small-and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.

  • 9.
    Innocenti, Nicolas
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Nguyen, Hoang-Son
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Fouquier d'Hérouël, Aymeric
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    An observation of circular RNAs in bacterial RNA-seq data.2015Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea. Here, we have analyzed RNA-seq data obtained from Enterococcus faecalis and Escherichia coli in a way similar to previous studies performed on eukaryotes. We report observations of circRNAs in RNA-seq data that are reproducible across multiple experiments performed with different protocols or growth conditions.

  • 10.
    Innocenti, Nicolas
    et al.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Mikroelektronik och tillämpad fysik, MAP.
    Popov, Sergei
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Mikroelektronik och tillämpad fysik, MAP.
    Sergeyev, Sergey
    Waterford Institute of Technology.
    Friberg, Ari
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Mikroelektronik och tillämpad fysik, MAP.
    External field enhancement in coupled polymer microcavities - New options for integrated photonic components2009Inngår i: European Conference on Lasers and Electro-Optics 2009 and the European Quantum Electronics Conference. CLEO Europe - EQEC 2009, 2009Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Microcavities are key components for integrated optical devices and systems. In this paper, enhancement of the resonance electric field outside a pair of coupled polymeric microcavities of hexagonal shape is investigated. Using numerical simulation, enhancement of outside-cavity field has been demonstrated in different sections of the coupled cavity system depending on particular design. Resonance frequencies are in visible part of electromagnetic spectrum. In reported simulations rigorous models based on solving Maxwell equations for propagating electromagnetic field in polymeric materials commonly used in nano-imprinting lithography is demonstrated.

  • 11.
    Innocenti, Nicolas
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Repoila, Francis
    INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France}\affiliation{AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bateria using tagRNA-seq2015Inngår i: RNA Biology, ISSN 1547-6286, E-ISSN 1555-8584Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Standard RNA-seq has a well know tendency to generate "ghost" antisense reads due to formation of spurious second strand cDNA in the sequencing process. We recently reported on a novel variant of RNA-seq coined "tagRNA-seq" introduced for the purpose of distinguishing primary from processed transcripts in bacteria. Incidentally, the additional information provided by the tag is also very suitable for detection of true anti-sense RNA transcripts and quantification of spurious antisense signals in a sample. We briefly explain how to perform such a detection and illustrate on previously published datasets.

  • 12. Koelling, S.
    et al.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Bogdanowicz, J.
    Vandervorst, W.
    Optimal laser positioning for laser-assisted atom probe tomography2013Inngår i: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 132, s. 70-74Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Laser-assisted atom probe tomography is a material analysis method based on field evaporating ions from a tip-shaped sample by a combination of a standing electric held and a short (pico- or lemtosecond) laser pulse. The laser-pulse thereby acts as a starting signal for a time-of-flight mass analysis of the ions whereby the thermal energy deposited in the tip by the laser pulse temporarily enables the evaporation of ions from the surface of the tip. Here we will use simulations of the laser absorption on a silicon tip to find the optimal position of the laser spot in order to maximize the mass resolution achieved during the experiments. We will confirm our simulations by showing that the experimentally observed mass resolution indeed changes as predicted by the simulations.

  • 13.
    Koelling, Sebastian
    et al.
    Imec, Kapeldreef 75, B-3000 Leuven, Belgium.
    Innocenti, Nicolas
    Imec, Kapeldreef 75, B-3000 Leuven, Belgium; University of Liege, Institut Montefiore .
    Hellings, Geert Hellings
    Imec, Kapeldreef 75, B-3000 Leuven, Belgium.
    Gilbert, Matthieu
    Imec, Kapeldreef 75, B-3000 Leuven, Belgium.
    Kambham, Ajay Kumar
    Imec, Kapeldreef 75, B-3000 Leuven, Belgium.
    De Meyer, Kristin
    Imec, Kapeldreef 75, B-3000 Leuven, Belgium.
    Vandervorst, Wilfried
    Imec, Kapeldreef 75, B-3000 Leuven, Belgium.
    Characteristics of cross-sectional atom probe analysis on semiconductor structures2011Inngår i: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 111, nr 6, s. 540-545Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The laser-assisted Atom Probe has been proposed as a metrology tool for next generation semiconductor technologies requiring sub-nm spatial resolution. In order to assess its potential for the analysis of three-dimensional semiconductor structures like FinFETs, we have studied the Atom Probes lateral resolution on a silicon, silicon–germanium multilayer structure. We find that the interactions of the laser with the semiconductor materials in the sample distort the sample surface. This results in transient errors of the measured dimensions of the structure. The deformation of the sample furthermore leads to a degradation of the lateral resolution. In the experiments presented in this paper, the Atom Probe reaches a lateral resolution of 1-1.8 nm/decade. In this paper we will discuss the reasons for the distortions of the tip and demonstrate that with the present state of data reconstruction severe quantification errors limit its applicability for the quantitative analysis of heterogeneous semiconductor structures. Our experiments show that reconstruction algorithms taking into account the time dependent nanostructure of the tip shape are required to arrive at accurate results.

  • 14.
    Koelling, Sebastian
    et al.
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Innocenti, Nicolas
    IMEC, B-3000 Louvain; Univ Liege, Inst Montefiore .
    Schulze, Andreas
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Gilbert, Matthieu
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Kambham, AJay Kumar
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Vandervorst, Wilfried
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    In-situ observation of non-hemispherical tip shape formation during laser-assisted atom probe tomography2011Inngår i: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 109, nr 10, s. 104909-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    It is shown by SEM imaging of the tip and by observing the emission pattern of the evaporated atoms that laser assisted evaporation in an atom probe can lead to nonhemispherical tip shapes and time-dependent nonuniform emission. We have investigated this nonuniformity by observing the change in field of view when using laser wavelengths of 515 nm and 343 nm on silicon. The change is monitored in situ by 0.5 nm thick silicon oxide. We demonstrate that the field of view can easily be changed by more than 10 nm and that the apparent oxide layer thickness can deviate substantially from its correct value. The dependence of the tip shape deformations and the reconstruction artifacts on the laser wavelength are explained through simulations of the laser-tip interaction and nonhomogeneous heating effects.

  • 15. Maes, Alexandre
    et al.
    Céline, Gracia
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Zhang, Kaiyang
    Aalto University, Finland .
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Hajnsdorf, Eliane
    Landscape of RNA polyadenylation in E. coli2016Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Polyadenylation is involved in degradation and quality control of bacterial RNAs. We used a combination of 5’-tagRACE and RNA-seq to analyse the total RNA content from wild-type strain and from mutant deficient for poly(A)polymerase. We determined that 157 mRNAs were affected as well as non-coding transcripts, up- and downregulated in the mutant when compared to the wild-type strain. Antisense RNAs were also detected and differentially affected by polyadenylation.

    Our results clearly reveal a correlation between the RNA folding energy and the requirement of polyadenylation to achieve the RNA decay. A new algorithm was developed to detect in both strains posttranscriptional modifications based on unmappable 3’-ends to analyse their position and composition. Therefore, any RNA 3'-end can be polyadenylated addressing them to the exoribonucleolytic machinery which is essential to degrade structured RNAs. Importantly, poly(A)polymerase was also upregulating the expression of genes related with the entire FliA regulon and numerous membrane transporters while downregulating the expression of the antigen 43 (flu), numerous sRNAs, antisense transcripts, REP sequences with the accumulation of numerous RNA fragments resulting from the processing of entire transcripts. Altogether we show here that polyadenylation has a broader spectrum of action than was suspected until now.

  • 16.
    Popov, Sergei
    et al.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Fotonik och optik (Stängd 20120101), Optik (Stängd 20120101).
    Dong, Lin
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Fotonik och optik (Stängd 20120101), Optik (Stängd 20120101).
    Innocenti, Nicolas
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Fotonik och optik (Stängd 20120101), Optik (Stängd 20120101).
    Sergeyev, Sergey
    Waterford Institute of Technology.
    Friberg, Ari
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Fotonik och optik (Stängd 20120101), Optik (Stängd 20120101).
    External near-field resonance in coupled microcavities: mode enhancement and applications2010Inngår i: 2010 Asia Communications and Photonics Conference and Exhibition, ACP 2010, 2010, s. 90-91Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Interference of the near optical field caused by evanescent waves leaking a coupled microcavity enhances the optical field between the cavity sections. This enhancement can be used for design of microcavity lasers with outside-cavity modes and for various sensors, for example, to precisely detect the direction of incident wavefront.

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